TL;DR -- Possibly it has to do with the style that I use, but those things doesn't actually happen to me very often, and when they do it's not a big deal. For me, the benefits of REPL-driven-development far outweigh occasionally having to deal with these issues.

Two things. First, I've been bitten by this myself, but it's pretty much always been something like "Oops, I renamed a function and forgot to update a reference to it, but the code still worked because the old definition was still there... until I reloaded the REPL." It's always been a trivial fix for me, since when I try to re-evaluate the buffer containing the outdated function reference it throws a "cannot find function definition" error. I currently consider the advantages of REPL-driven development to outweigh that occasionally happening.

Second thing: maybe others do it differently, but I don't think I generally make manual changes to the state while things are running. If the state doesn't look the way it should, I either start iteratively tweaking functions (by modifying my .clj file and eval-ing them) and re-running with fresh state to understand and resolve the problem, or I work with a separate, similarly-shaped piece of state and run it through functions in a sort of "manual unit testing" to tweak and fix whatever's wrong, and then I re-run everything from scratch to make sure it worked. I don't adjust the state, evaluate a code path, and then continue on if it works (because yeah, I can totally see how that would lead to the sort of situation you describe, which sounds unpleasant)